Context dependence of protein secondary structure formation: The three-dimensional structure and stability of a hybrid between chymotrypsin inhibitor 2 and helix E from subtilisin Carlsberg

Biochemistry ◽  
1993 ◽  
Vol 32 (41) ◽  
pp. 11007-11014 ◽  
Author(s):  
Peter Osmark ◽  
Poul Soerensen ◽  
Flemming M. Poulsen
Keyword(s):  
Secondary Structure ◽  
Structure Formation ◽  
Three Dimensional ◽  
Protein Secondary Structure ◽  
Context Dependence ◽  
Dimensional Structure ◽  
Chymotrypsin Inhibitor ◽  
Secondary Structure Formation ◽  
Subtilisin Carlsberg ◽  
Chymotrypsin Inhibitor 2

scholarly journals ATP-induced asymmetric pre-protein folding: a driver of protein translocation?

2017 ◽  
Author(s):  
Robin A. Corey ◽  
William J. Allen ◽  
Ian Collinson
Keyword(s):  
Secondary Structure ◽  
Structure Formation ◽  
Protein Transport ◽  
Protein Translocation ◽  
Protein Secondary Structure ◽  
Structural Data ◽  
Underlying Mechanism ◽  
Dynamics Simulation ◽  
Secondary Structure Formation ◽  
Atp Binding And Hydrolysis

AbstractThe transport of proteins across membranes is a fundamental and essential process, achieved in every cell by the ‘Sec’ translocon. In prokaryotes, SecYEG associates with the motor protein SecA to carry out ATP-driven pre-protein secretion – a vital step in the biogenesis of most periplasmic, outer membrane and secreted proteins. Structural data of the SecA-SecYEG complex has provided considerable insight into underlying mechanism of this process. Previously, we have proposed a Brownian ratchet model for protein translocation, whereby the free energy of ATP binding and hydrolysis favours the progression of pre-protein across the membrane from the cytosol toward the outside [Allen, Corey et al. eLife 2016]. Here, we use atomistic molecular dynamics simulation of a SecA-SecYEG complex engaged with preprotein to further address the mechanism underlying this process. The data describe pre-protein secondary structure formation within the channel, which exhibits a nucleotide-dependent asymmetry between the cytoplasmic and exterior cavities. The results suggest ATP-dependent pre-protein transport is partly driven by pre-protein secondary structure formation. The model previously described, and refined here, could easily be adapted for the transport of proteins across various other membranes, such as the endoplasmic reticular and mitochondrial inner membranes.

Dimensionality reduction for protein secondary structure and solvent accesibility prediction

2018 ◽  
Vol 16 (05) ◽  
pp. 1850020 ◽  
Author(s):  
Zafer Aydin ◽  
Oğuz Kaynar ◽  
Yasin Görmez
Keyword(s):  
Secondary Structure ◽  
Dimensionality Reduction ◽  
Solvent Accessibility ◽  
Three Dimensional ◽  
Protein Secondary Structure ◽  
Extraction Methods ◽  
Dimensional Structure ◽  
Support Vector ◽  
Noise Elimination ◽  
Solvent Accessibility Prediction

Secondary structure and solvent accessibility prediction provide valuable information for estimating the three dimensional structure of a protein. As new feature extraction methods are developed the dimensionality of the input feature space increases steadily. Reducing the number of dimensions provides several advantages such as faster model training, faster prediction and noise elimination. In this work, several dimensionality reduction techniques have been employed including various feature selection methods, autoencoders and PCA for protein secondary structure and solvent accessibility prediction. The reduced feature set is used to train a support vector machine at the second stage of a hybrid classifier. Cross-validation experiments on two difficult benchmarks demonstrate that the dimension of the input space can be reduced substantially while maintaining the prediction accuracy. This will enable the incorporation of additional informative features derived for predicting the structural properties of proteins without reducing the accuracy due to overfitting.

In Silico Study of Secondary Structure of Hemoglobin Protein

2021 ◽  
pp. 6245-6249
Author(s):  
Roma Chandra
Keyword(s):  
Secondary Structure ◽  
Protein Sequence ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Secondary Structure Prediction ◽  
Three Dimensional ◽  
Protein Secondary Structure ◽  
Alpha Helix ◽  
Prediction Methods ◽  
Protein Secondary Structures

Protein structure prediction is one of the important goals in the area of bioinformatics and biotechnology. Prediction methods include structure prediction of both secondary and tertiary structures of protein. Protein secondary structure prediction infers knowledge related to presence of helixes, sheets and coils in a polypeptide chain whereas protein tertiary structure prediction infers knowledge related to three dimensional structures of proteins. Protein secondary structures represent the possible motifs or regular expressions represented as patterns that are predicted from primary protein sequence in the form of alpha helix, betastr and and coils. The secondary structure prediction is useful as it infers information related to the structure and function of unknown protein sequence. There are various secondary structure prediction methods used to predict about helixes, sheets and coils. Based on these methods there are various prediction tools under study. This study includes prediction of hemoglobin using various tools. The results produced inferred knowledge with reference to percentage of amino acids participating to produce helices, sheets and coils. PHD and DSC produced the best of the results out of all the tools used.

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